Category:Model repositories

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Building repositories of computational models of biological systems ensures that published models are available for both education and further research, and can provide a source of smaller, previously verified models to integrate into a larger model [1].

Repository, URL, references Number of models, format Brief description
CellML model repository [2]

http://models.cellml.org

500+

CellML

The CellML Model Repository provides free access to 500+ biological models. The vast majority of these models are derived from published, peer-reviewed papers. Model curation is an important and ongoing process to ensure the CellML model is able to accurately reproduce the published results.


Physiome Repository [3]

https://models.physiomeproject.org

500+

CellML, FieldML

The Auckland Physiome Repository provides extensive support for CellML model and related files. Previously it was called the CellML Model Repository, this has since been merged completely along with the FieldML Model Repository into the unified repository. The underlying software is PMR2, which in turn relies on the distributed version control system Mercurial (Hg), which allows the repository to maintain a complete history of all changes made to every file it contains.

References

  1. Miller AK, Yu T, Britten R, Cooling MT, Lawson J, Cowan D, Garny A, Halstead MD, Hunter PJ, Nickerson DP, Nunns G, Wimalaratne SM, and Nielsen PM. Revision history aware repositories of computational models of biological systems. BMC Bioinformatics. 2011 Jan 14;12:22. DOI:10.1186/1471-2105-12-22 | PubMed ID:21235804 | HubMed [Miller2011]
  2. Lloyd CM, Lawson JR, Hunter PJ, and Nielsen PF. The CellML Model Repository. Bioinformatics. 2008 Sep 15;24(18):2122-3. DOI:10.1093/bioinformatics/btn390 | PubMed ID:18658182 | HubMed [Lloyd2008]
  3. Yu T, Lloyd CM, Nickerson DP, Cooling MT, Miller AK, Garny A, Terkildsen JR, Lawson J, Britten RD, Hunter PJ, and Nielsen PM. The Physiome Model Repository 2. Bioinformatics. 2011 Mar 1;27(5):743-4. DOI:10.1093/bioinformatics/btq723 | PubMed ID:21216774 | HubMed [Yu2011]
All Medline abstracts: PubMed | HubMed

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